Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate Synpcc7942_1927 Synpcc7942_1927 diaminopimelate epimerase
Query= SwissProt::Q81XR2 (288 letters) >FitnessBrowser__SynE:Synpcc7942_1927 Length = 280 Score = 209 bits (532), Expect = 6e-59 Identities = 119/281 (42%), Positives = 166/281 (59%), Gaps = 11/281 (3%) Query: 6 FTKMHGLGNSYIYVNMFEEQIPEEDLALVAEKVSNINTGIGADGMILICP-SDVAPVKMR 64 F K HGLGN +I V+ E P A +V + N G+GADG+I P S + MR Sbjct: 5 FAKYHGLGNDFILVDNRESGEPRLTPEQ-AVQVCDRNFGVGADGVIFALPGSGDSDYVMR 63 Query: 65 MFNNDGSEGKSCGNGLRCVAKYAYEHKLVEDTVFTIETLAGIVTAEVTVEEGKVTLAKID 124 +FN+DGSE + CGNG+RC+AK+ E + + I T AG++ +T E G VT +D Sbjct: 64 IFNSDGSEPEMCGNGIRCLAKFLSELDGGAQSRYRIATGAGLIVPTLT-ETGLVT---VD 119 Query: 125 MGAPRLTRAEIP--MLGEGETPFIRENFLYNNHRYAFTAVSMGNPHAVIFVDDVEQAPLT 182 MG L EIP + G G+ + + + + T VSMGNPH + FV+DV PL Sbjct: 120 MGPAYLKPVEIPTTLTGTGDR-VVEADLEVGDRPWKVTTVSMGNPHCITFVEDVAAVPLA 178 Query: 183 TLGPVLETHEMFPERVNVEFIEILNEEEMNFRVWERGSGVTQACGTGACAAVVASILNGK 242 +GP+ E H +FP+R N EF+E++ + + RVWERG+G T ACGTGACA +VA++L G+ Sbjct: 179 EIGPLFEHHPVFPQRTNTEFVEVVRPDYLKMRVWERGAGATLACGTGACATLVAAVLTGR 238 Query: 243 MERGKEITVHLAGGDLMIAWTEEGNVLMKGPAEVICRGVYE 283 +R + TV L GG L I W E+G++ M GPA + G E Sbjct: 239 SDR--QATVELPGGPLQIEWREDGHLFMTGPAVKVFSGSME 277 Lambda K H 0.318 0.136 0.398 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 240 Number of extensions: 11 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 288 Length of database: 280 Length adjustment: 26 Effective length of query: 262 Effective length of database: 254 Effective search space: 66548 Effective search space used: 66548 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
Align candidate Synpcc7942_1927 Synpcc7942_1927 (diaminopimelate epimerase)
to HMM TIGR00652 (dapF: diaminopimelate epimerase (EC 5.1.1.7))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00652.hmm # target sequence database: /tmp/gapView.26411.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00652 [M=270] Accession: TIGR00652 Description: DapF: diaminopimelate epimerase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-99 318.5 0.0 2.1e-99 318.3 0.0 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_1927 Synpcc7942_1927 diaminopimelate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_1927 Synpcc7942_1927 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 318.3 0.0 2.1e-99 2.1e-99 2 268 .. 4 276 .. 3 278 .. 0.96 Alignments for each domain: == domain 1 score: 318.3 bits; conditional E-value: 2.1e-99 TIGR00652 2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvepsseeadvklrifNsDGSea 70 +F+k+hGlgNdF+lvd++++ ++ ++e++ +vcdr++gvgaDgv++ p+s + d+ +rifNsDGSe+ lcl|FitnessBrowser__SynE:Synpcc7942_1927 4 QFAKYHGLGNDFILVDNRESGEPRLTPEQAVQVCDRNFGVGADGVIFALPGSGDSDYVMRIFNSDGSEP 72 8*******************9*9999******************************************* PP TIGR00652 71 emCGNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeek 139 emCGNgiRc+akf+ e + ++++++ t agli+ +++e++ v+vdmg + +k+ eip+t +++ + lcl|FitnessBrowser__SynE:Synpcc7942_1927 73 EMCGNGIRCLAKFLSELDGGAQSRYRIATGAGLIVPTLTETG-LVTVDMGPAYLKPVEIPTTLTGTGDR 140 ****************999999********************.*******************8777776 PP TIGR00652 140 eellalev......l.vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeikl 201 + + lev + v++GnPH+++fvedv ++l e+g+l+e+h+ fp+++N+efvev+ +d +k+ lcl|FitnessBrowser__SynE:Synpcc7942_1927 141 VVEADLEVgdrpwkVtTVSMGNPHCITFVEDVAAVPLAEIGPLFEHHPVFPQRTNTEFVEVVRPDYLKM 209 6666666677786537***************************************************** PP TIGR00652 202 rvyERGageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedgkvyltGpavlvlegel 268 rv+ERGag TlaCGtGa+A+ v+a+ +g++++++tv+l+gg L+ie++edg++++tGpav+v++g + lcl|FitnessBrowser__SynE:Synpcc7942_1927 210 RVWERGAGATLACGTGACATLVAAVLTGRSDRQATVELPGGPLQIEWREDGHLFMTGPAVKVFSGSM 276 ****************************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (280 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6.49 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory